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- PDB-9gcm: Structure of the U11 snRNP core -

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Basic information

Entry
Database: PDB / ID: 9gcm
TitleStructure of the U11 snRNP core
Components
  • Programmed cell death protein 7
  • U11 snRNA
  • U11/U12 small nuclear ribonucleoprotein 25 kDa protein
  • U11/U12 small nuclear ribonucleoprotein 35 kDa protein
KeywordsSPLICING / minor spliceosome / U11 snRNP / RNA-protein complex
Function / homology
Function and homology information


snRNA binding / U12-type spliceosomal complex / mRNA Splicing - Minor Pathway / intercellular bridge / response to glucocorticoid / RNA splicing / mRNA splicing, via spliceosome / mRNA binding / apoptotic process / nucleolus ...snRNA binding / U12-type spliceosomal complex / mRNA Splicing - Minor Pathway / intercellular bridge / response to glucocorticoid / RNA splicing / mRNA splicing, via spliceosome / mRNA binding / apoptotic process / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Programmed cell death protein 7 / snRNP35, RNA recognition motif / : / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25kDa protein / SNRNP25, ubiquitin-like domain / Ubiquitin-like domain / : / RNA recognition motif / RNA recognition motif ...Programmed cell death protein 7 / snRNP35, RNA recognition motif / : / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25kDa protein / SNRNP25, ubiquitin-like domain / Ubiquitin-like domain / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / U11/U12 small nuclear ribonucleoprotein 35 kDa protein / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhao, J. / Galej, W.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)950278European Union
CitationJournal: Mol Cell / Year: 2025
Title: Structural basis of 5' splice site recognition by the minor spliceosome.
Authors: Jiangfeng Zhao / Daniel Peter / Irina Brandina / Xiangyang Liu / Wojciech P Galej /
Abstract: The minor spliceosome catalyzes excision of U12-dependent introns from precursors of eukaryotic messenger RNAs (pre-mRNAs). This process is critical for many cellular functions, but the underlying ...The minor spliceosome catalyzes excision of U12-dependent introns from precursors of eukaryotic messenger RNAs (pre-mRNAs). This process is critical for many cellular functions, but the underlying molecular mechanisms remain elusive. Here, we report a cryoelectron microscopy (cryo-EM) reconstruction of the 13-subunit human U11 small nuclear ribonucleoprotein particle (snRNP) complex in apo and substrate-bound forms, revealing the architecture of the U11 small nuclear RNA (snRNA), five minor spliceosome-specific factors, and the mechanism of the U12-type 5' splice site (5'SS) recognition. SNRNP25 and SNRNP35 specifically recognize U11 snRNA, while PDCD7 bridges SNRNP25 and SNRNP48, located at the distal ends of the particle. SNRNP48 and ZMAT5 are positioned near the 5' end of U11 snRNA and stabilize binding of the incoming 5'SS. Recognition of the U12-type 5'SS is achieved through base-pairing to the 5' end of the U11 snRNA and unexpected, non-canonical base-triple interactions with the U11 snRNA stem-loop 3. Our structures provide mechanistic insights into U12-dependent intron recognition and the evolution of the splicing machinery.
History
DepositionAug 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U11 snRNA
B: U11/U12 small nuclear ribonucleoprotein 25 kDa protein
C: U11/U12 small nuclear ribonucleoprotein 35 kDa protein
D: Programmed cell death protein 7


Theoretical massNumber of molelcules
Total (without water)143,1034
Polymers143,1034
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain U11 snRNA


Mass: 43505.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: GenBank: 161169046
#2: Protein U11/U12 small nuclear ribonucleoprotein 25 kDa protein / U11/U12 snRNP 25 kDa protein / U11/U12-25K / Minus-99 protein


Mass: 15290.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP25, C16orf33 / Production host: Homo sapiens (human) / References: UniProt: Q9BV90
#3: Protein U11/U12 small nuclear ribonucleoprotein 35 kDa protein / U11/U12 snRNP 35 kDa protein / U11/U12-35K / Protein HM-1 / U1 snRNP-binding protein homolog


Mass: 29514.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP35, HM1, U1SNRNPBP / Production host: Homo sapiens (human) / References: UniProt: Q16560
#4: Protein Programmed cell death protein 7 / ES18 / hES18


Mass: 54791.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD7 / Production host: Homo sapiens (human) / References: UniProt: Q8N8D1
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the U11 snRNP core / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9 / Details: 20 mM HEPES-KOH, pH 7.9 200 mM KCl 2 mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMpotassium chlorideKCl1
22 mMmagnesium chlorideMgCl21
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Preliminary grid screening was performed on Glacios.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41.73 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 30164 / Details: Images were colleted in EER format
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.1particle selection
2SerialEMimage acquisition
7UCSF ChimeraX1.6.1model fitting
9cryoSPARCv4.3.1initial Euler assignment
10cryoSPARCv4.3.1final Euler assignment
11cryoSPARCv4.3.1classification
12cryoSPARCv4.3.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 7144222 / Details: Topaz picking is performed with user-trained model
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268233 / Symmetry type: POINT
Atomic model buildingB value: 71.2 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correction coefficient / Details: refinement is done in Phenix
Atomic model building

3D fitting-ID: 1 / Source name: AlphaFold / Type: in silico model

IDAccession codeChain-IDChain residue rangeInitial refinement model-ID
1AF-Q9BV90-F1B1-1321
2AF-Q16560-F1C1-2462
3AF-Q8N8D1-F1D1-4853

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